Done.
-parsing GTF file: /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.kUMntwtXBN/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00613_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00613_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:56:47 : INFO : Done.
-parsing GTF file: /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1020000] -done parsing /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 177,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'per_id < 96' => 2968,
'seq-similar region overlap' => 24,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 303,
'small anchor length' => 1,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
'excessive soft clipping' => 6719,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 52,
' ** passed ** ' => 1724,
'num genes matched < 2' => 70
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[14000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[160000] -fusion SPANNING read extraction for scaff: KIAA1217--AL512598.1
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[41000] -fusion SPANNING read extraction for scaff: NUP210--SYN2
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[41000] -fusion SPANNING read extraction for scaff: NUP210--GSTM5P1
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[6000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[13000] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146
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[128000] -fusion SPANNING read extraction for scaff: RNF135--NF1
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[63000] -fusion SPANNING read extraction for scaff: ROCK1--MIR663AHG
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[63000] -fusion SPANNING read extraction for scaff: ROCK1--FRG1CP
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[70000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[20000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[77000] -fusion SPANNING read extraction for scaff: TRIM33--AL121999.1
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[16000] -fusion SPANNING read extraction for scaff: TRIM59--IFT80
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[11000] -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 5953,
'seq similar region alignment' => 4652
};
EM: Starting log likelihood: -2800.335641
EM: Round [1] log likelihood: -2799.105686
EM: Round [2] log likelihood: -2798.718005
EM: Round [3] log likelihood: -2798.424756
EM: Round [4] log likelihood: -2798.196429
EM: Round [5] log likelihood: -2798.017183
EM: Round [6] log likelihood: -2797.875604
EM: Round [7] log likelihood: -2797.763246
EM: Round [8] log likelihood: -2797.673746
EM: Round [9] log likelihood: -2797.602243
EM: Round [10] log likelihood: -2797.544983
EM: Round [11] log likelihood: -2797.499041
EM: Round [12] log likelihood: -2797.462122
EM: Round [13] log likelihood: -2797.432417
EM: Round [14] log likelihood: -2797.408489
EM: Round [15] log likelihood: -2797.389196
EM: Round [16] log likelihood: -2797.373629
EM: Round [17] log likelihood: -2797.361059
EM: Round [18] log likelihood: -2797.350902
EM: Round [19] log likelihood: -2797.342690
EM: Round [20] log likelihood: -2797.336046
EM: Round [21] log likelihood: -2797.330667
EM: Round [22] log likelihood: -2797.326310
EM: Round [23] log likelihood: -2797.322779
EM: Round [24] log likelihood: -2797.319914
EM: Round [25] log likelihood: -2797.317589
EM: Round [26] log likelihood: -2797.315700
EM: Round [27] log likelihood: -2797.314163
EM: Round [28] log likelihood: -2797.312913
EM: Round [29] log likelihood: -2797.311894
EM: Round [30] log likelihood: -2797.311063
EM: Round [31] log likelihood: -2797.310384
EM: Round [32] log likelihood: -2797.309829
EM: Round [33] log likelihood: -2797.309374
EM: Round [34] log likelihood: -2797.309000
EM: Round [35] log likelihood: -2797.308693
EM: Round [36] log likelihood: -2797.308439
EM: Round [37] log likelihood: -2797.308230
EM: Round [38] log likelihood: -2797.308057
EM: Round [39] log likelihood: -2797.307913
EM: Round [40] log likelihood: -2797.307793
EM: Round [41] log likelihood: -2797.307692
EM: Round [42] log likelihood: -2797.307608
EM: Stopping iterations at round 42 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.kUMntwtXBN/fi_workdir/tih_rna_sample_00613_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2719.044861
EM: Round [1] log likelihood: -2718.856761
EM: Round [2] log likelihood: -2718.856314
EM: Round [3] log likelihood: -2718.856312
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1_1.fastp.fastq.gz: 296056639
Warning - not locating file: /tmp/nxf.kUMntwtXBN/tih_rna_sample_00613_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000232895.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000229563.7]
WARNING, no entry stored in dbm for [ENSG00000229563.7]
WARNING, no entry stored in dbm for [ENSG00000229563.7]
WARNING, no entry stored in dbm for [ENSG00000229563.7]
ls: cannot access 'IGV_inputs': No such file or directory